Decoding Cell Communication

Understanding the Functions and Mechanisms of Every Aspect of the Cell Nucleus Now Viewed as Critical

The eukaryotic translation initiation factor (eIF4E) in primary cells as seen by confocal laser microscopy

The intricate interplay of cellular signaling pathways provides a beehive of biologic activity in the nucleus. Understanding how these pathways function and dysfunction not only helps trace the roots of cancers and genetic disorders but also suggests new therapeutic targets. At the recently held Gordon Conference on “Signal Transduction within the Nucleus,” GEN spoke with several presenters who shared their insights into this cutting-edge field.

“Behold the awesome power of yeast genetics and biochemistry,” proclaimed Ali Shilatifard, Ph.D., investigator with the Stowers Institute, as he began his keynote address. Dr. Shilatifard, who also was a co-organizer of the conference, described lessons learned from yeast about human leukemia. “My research focuses on work related to lymphocytic leukemia and mixed-lineage leukemia (MLL).

“This childhood cancer results from translocations in the MLL gene on chromosome 11. For unknown reasons, the gene appears to break in infancy. Its translocation causes leukemia with a very poor prognosis. This gene was discovered over 25 years ago by clinicians, however for a long time we did not understand its function. Therefore, we decided to take the road less traveled and use yeast as a model system to investigate the molecular functions of the MLL homologue.”

According to Dr. Shilatifard, Saccharomyces cerevisiae expresses an MLL homologue called Set1. “Yeast has been a great model system to begin dissecting our way through this pathway. We found that Set1 is a component of a larger complex we named COMPASS (complex proteins associated with Set1). Human MLL is also found in a COMPASS-like complex. Further, we determined that COMPASS can modify histone methylation, and based on these findings it was demonstrated that the MLL complex is also a histone methylase. This gives us clues as to how to find possible therapeutic targets. For example, inhibiting or modulating methylation/demethylation could be the basis for targeted treatments.”

Lately, model systems have been ignored and sidelined by funding agencies in favor of translational studies, noted Dr. Shilatifard. “I think some people do not understand the absolute power of a model system. Sarah Palin, for example, asked why should we study fruit flies. However, Drosophila, yeast, zebrafish, and other simple model systems all have the capacity to provide us with much-needed information.”

Chromatin Remodeling Complexes

Within a cell nucleus, chromosomal DNA is tightly wound and intertwined with proteins known as histones and assembled in histone/DNA units called nucleosomes, similar to beads on a string. These strands are collectively known as chromatin. “It is the chromatin that needs to be modified and dealt with, not naked DNA, to allow access by transcription factors and DNA repair machinery,” said Xuetong Shen, Ph.D., associate professor, department of carcinogenesis, M.D. Anderson Cancer Center.

Dr. Shen’s laboratory focuses on understanding the functions and mechanisms of a family of novel chromatin-remodeling complexes called INO80. “Basically, INO80 moves the beads around to expose DNA. Traditionally, people thought of chromatin remodeling primarily as a means for transcription, but we now see that chromatin remodeling is involved in DNA repair as well. When not repaired properly, cancer may result. This provides us with a potential new target for the detection, prevention, and treatment of cancer.”

The next goal of Dr. Shen’s group is to further dissect and understand mechanistically how chromatin remodeling functions in maintaining genome integrity. “We expect to use whole-genome analysis to determine where the INO80 complex binds and how it functions to prevent DNA damage,” reported Karina Falbo, a Ph.D. candidate in the Shen laboratory. “In the long term, we will also be pursuing the link to cancer by developing a mouse model to assess its possible role in causing cancer.”

According to Dr. Shen, one of the take-home messages of this work is “that we are just beginning to realize that chromatin carries a lot of information. Chromatin remodeling is likely to be involved in epigenetic changes. Understanding the function and mechanism of how these players exert their influence in the nucleus has important implications for our understanding not only about chromatin but also about the basic functions within the nucleus itself.”

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